DNA DNA Double-strand Breaks Repair Pathway Research Articles

Abstract IA015: Using systems approaches to interrogate DNA double strand break signaling and repair for optimal tumor cell killing

Abstract Repair of DNA double strand breaks (DSBs) occurs through multiple distinct repair pathways including canonical and microhomology-mediated/Pol Q-dependent end joining (c-NHEJ and alt-NHEJ), homologous recombination (HR), and single strand annealing (SSA). Exactly how a particular DSB dictates which pathway is selected for repair, and the extent to which different DSB repair pathways cross-talk with each other is incompletely understood, but appears to be influenced by the specific type of DNA ends, the extent of DNA resection, the cell state and stage of the cell cycle, and the chromatin context around the break. To simultaneously interrogate multiple DNA DSB repair pathways in a systems-based manner at the single cell level, we built upon the pioneering DSB repair reporter systems created by the Jasin, Stark, Scharenberg and Certo labs to create several new CRISPR-based DNA DSB reporter systems that readout the repair of a single genomic DNA DSB by error-free c-NHEJ, mutagenic c- and alt-NHEJ, HR or SSA using multi-color fluorescence-based imaging and flow cytometry approaches. Using these DSB reporter systems we show that competition between short-range and long-range end resection influences the choice between repair by HR versus SSA, demonstrate accepted and novel functions for a variety of DNA damage sensors and repair proteins in NHEJ and HR, and illustrate the feasibility of using this system to interrogate the effects of patient-specific mutations in DNA repair proteins on DNA DSB repair pathway choice. Finally, we show that DNA DSBs created by topoisomerase inhibitor treatment in live but DNA-damaged tumor cells are capable of activating anti-tumor immune responses by signaling through both canonical and non-canonical DNA break sensing and response pathways. Citation Format: Alex Kruswick, Bert van de Kooij, Tiffany R. Emmons, Ganapathy Sriram, Emma D. Martin, Anjali Arvind, Haico van Attikum, Michael B. Yaffe. Using systems approaches to interrogate DNA double strand break signaling and repair for optimal tumor cell killing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr IA015.

A Flow Cytometry-Based Method for Analyzing DNA End Resection in G0- and G1-Phase Mammalian Cells.

DNA double strand breaks (DSBs) constantly arise in cells during normal cellular processes or upon exposure to genotoxic agents, and are repaired mostly by homologous recombination (HR) and non-homologous end joining (NHEJ). One key determinant of DNA DSB repair pathway choice is the processing of broken DNA ends to generate single strand DNA (ssDNA) overhangs, a process termed DNA resection. The generation of ssDNA overhangs commits DSB repair through HR and inhibits NHEJ. Therefore, DNA resection must be carefully regulated to avoid mis-repaired or persistent DSBs. Accordingly, many approaches have been developed to monitor ssDNA generation in cells to investigate genes and pathways that regulate DNA resection. Here we describe a flow cytometric approach measuring the levels of replication protein A (RPA) complex, a high affinity ssDNA binding complex composed of three subunits (RPA70, RPA32, and RPA14 in mammals), on chromatin after DNA DSB induction to assay DNA resection. This flow cytometric assay requires only conventional flow cytometers and can easily be scaled up to analyze a large number of samples or even for genetic screens of pooled mutants on a genome-wide scale. We adopt this assay in G0- and G1- phase synchronized cells where DNA resection needs to be kept in check to allow normal NHEJ.

Regulation of the Cell-Intrinsic DNA Damage Response by the Innate Immune Machinery.

Maintenance of genomic integrity is crucial for cell survival. As such, elegant DNA damage response (DDR) systems have evolved to ensure proper repair of DNA double-strand breaks (DSBs) and other lesions that threaten genomic integrity. Towards this end, most therapeutic studies have focused on understanding of the canonical DNA DSB repair pathways to enhance the efficacy of DNA-damaging therapies. While these approaches have been fruitful, there has been relatively limited success to date and potential for significant normal tissue toxicity. With the advent of novel immunotherapies, there has been interest in understanding the interactions of radiation therapy with the innate and adaptive immune responses, with the ultimate goal of enhancing treatment efficacy. While a substantial body of work has demonstrated control of the immune-mediated (extrinsic) responses to DNA-damaging therapies by several innate immune pathways (e.g., cGAS–STING and RIG-I), emerging work demonstrates an underappreciated role of the innate immune machinery in directly regulating tumor cell-intrinsic/cell-autonomous responses to DNA damage.

A repackaged CRISPR platform increases homology-directed repair for yeast engineering.

Inefficient homology-directed repair (HDR) constrains CRISPR-Cas9 genome editing in organisms that preferentially employ nonhomologous end joining (NHEJ) to fix DNA double-strand breaks (DSBs). Current strategies used to alleviate NHEJ proficiency involve NHEJ disruption. To confer precision editing without NHEJ disruption, we identified the shortcomings of the conventional CRISPR platforms and developed a CRISPR platform-lowered indel nuclease system enabling accurate repair (LINEAR)-which enhanced HDR rates (to 67-100%) compared to those in previous reports using conventional platforms in four NHEJ-proficient yeasts. With NHEJ preserved, we demonstrate its ability to survey genomic landscapes, identifying loci whose spatiotemporal genomic architectures yield favorable expression dynamics for heterologous pathways. We present a case study that deploys LINEAR precision editing and NHEJ-mediated random integration to rapidly engineer and optimize a microbial factory to produce (S)-norcoclaurine. Taken together, this work demonstrates how to leverage an antagonizing pair of DNA DSB repair pathways to expand the current collection of microbial factories.

The Determinant of DNA Repair Pathway Choices in Ionising Radiation-Induced DNA Double-Strand Breaks.

Ionising radiation- (IR-) induced DNA double-strand breaks (DSBs) are considered to be the deleterious DNA lesions that pose a serious threat to genomic stability. The major DNA repair pathways, including classical nonhomologous end joining, homologous recombination, single-strand annealing, and alternative end joining, play critical roles in countering and eliciting IR-induced DSBs to ensure genome integrity. If the IR-induced DNA DSBs are not repaired correctly, the residual or incorrectly repaired DSBs can result in genomic instability that is associated with certain human diseases. Although many efforts have been made in investigating the major mechanisms of IR-induced DNA DSB repair, it is still unclear what determines the choices of IR-induced DNA DSB repair pathways. In this review, we discuss how the mechanisms of IR-induced DSB repair pathway choices can operate in irradiated cells. We first briefly describe the main mechanisms of the major DNA DSB repair pathways and the related key repair proteins. Based on our understanding of the characteristics of IR-induced DNA DSBs and the regulatory mechanisms of DSB repair pathways in irradiated cells and recent advances in this field, We then highlight the main factors and associated challenges to determine the IR-induced DSB repair pathway choices. We conclude that the type and distribution of IR-induced DSBs, chromatin state, DNA-end structure, and DNA-end resection are the main determinants of the choice of the IR-induced DNA DSB repair pathway.

Dipeptide repeat proteins inhibit homology-directed DNA double strand break repair in C9ORF72 ALS/FTD

BackgroundThe C9ORF72 hexanucleotide repeat expansion is the most common known genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two fatal age-related neurodegenerative diseases. The C9ORF72 expansion encodes five dipeptide repeat proteins (DPRs) that are produced through a non-canonical translation mechanism. Among the DPRs, proline-arginine (PR), glycine-arginine (GR), and glycine-alanine (GA) are the most neurotoxic and increase the frequency of DNA double strand breaks (DSBs). While the accumulation of these genotoxic lesions is increasingly recognized as a feature of disease, the mechanism(s) of DPR-mediated DNA damage are ill-defined and the effect of DPRs on the efficiency of each DNA DSB repair pathways has not been previously evaluated.Methods and resultsUsing DNA DSB repair assays, we evaluated the efficiency of specific repair pathways, and found that PR, GR and GA decrease the efficiency of non-homologous end joining (NHEJ), single strand annealing (SSA), and microhomology-mediated end joining (MMEJ), but not homologous recombination (HR). We found that PR inhibits DNA DSB repair, in part, by binding to the nucleolar protein nucleophosmin (NPM1). Depletion of NPM1 inhibited NHEJ and SSA, suggesting that NPM1 loss-of-function in PR expressing cells leads to impediments of both non-homologous and homology-directed DNA DSB repair pathways. By deleting NPM1 sub-cellular localization signals, we found that PR binds NPM1 regardless of the cellular compartment to which NPM1 was directed. Deletion of the NPM1 acidic loop motif, known to engage other arginine-rich proteins, abrogated PR and NPM1 binding. Using confocal and super-resolution immunofluorescence microscopy, we found that levels of RAD52, a component of the SSA repair machinery, were significantly increased iPSC neurons relative to isogenic controls in which the C9ORF72 expansion had been deleted using CRISPR/Cas9 genome editing. Western analysis of post-mortem brain tissues confirmed that RAD52 immunoreactivity is significantly increased in C9ALS/FTD samples as compared to controls.ConclusionsCollectively, we characterized the inhibitory effects of DPRs on key DNA DSB repair pathways, identified NPM1 as a facilitator of DNA repair that is inhibited by PR, and revealed deficits in homology-directed DNA DSB repair pathways as a novel feature of C9ORF72-related disease.

FKBP25 participates in DNA double-strand break repair.

FK506-binding proteins (FKBPs) alter the conformation of proteins via cis-trans isomerization of prolyl-peptide bonds. While this activity can be demonstrated in vitro, the intractability of detecting prolyl isomerization events in cells has limited our understanding of the biological processes regulated by FKBPs. Here we report that FKBP25 is an active participant in the repair of DNA double-strand breaks (DSBs). FKBP25 influences DSB repair pathway choice by promoting homologous recombination (HR) and suppressing single-strand annealing (SSA). Consistent with this observation, cells depleted of FKBP25 form fewer Rad51 repair foci in response to etoposide and ionizing radiation, and they are reliant on the SSA repair factor Rad52 for viability. We find that FKBP25’s catalytic activity is required for promoting DNA repair, which is the first description of a biological function for this enzyme activity. Consistent with the importance of the FKBP catalytic site in HR, rapamycin treatment also impairs homologous recombination, and this effect is at least in part independent of mTor. Taken together these results identify FKBP25 as a component of the DNA DSB repair pathway.

A Versatile Tool for the Quantification of CRISPR/Cas9-Induced Genome Editing Events in Human Hematopoietic Cell Lines and Hematopoietic Stem/Progenitor Cells

The efficient site-specific DNA double-strand breaks (DSB) created by CRISPR/Cas9 has revolutionized genome engineering and has great potential for editing hematopoietic stem/progenitor cells (HSPCs). However, detailed understanding of the variables that influence choice of DNA–DSB repair (DDR) pathways by HSPC is required for therapeutic levels of editing in these clinically relevant cells. We developed a hematopoietic-reporter system that rapidly quantifies the three major DDR pathways utilized at the individual DSB created by CRISPR/Cas9—NHEJ, MMEJ, and HDR—and show its applicability in evaluating the different DDR outcomes utilized by human hematopoietic cell lines and primary human HSPC.

Refining Radiation for the Next Century.

![][1] Wilhelm Roentgen's report more than a century ago describing X-ray imaging fostered in the application of ionizing radiation (IR) for cancer therapy. Today, about half of all the patients with cancer are treated with radiotherapy and it remains one of our most effective

Abstract 4145: Concurrent treatment with Pim kinase inhibitor decreases alternative non-homologous end-joining repair of DNA damage induced by topoisomerase 2 inhibitors in cells with FLT3-ITD

Abstract Purpose: Internal tandem duplication of fms-like tyrosine kinase 3 (FLT3-ITD) is a common (30%) molecular abnormality in acute myeloid leukemia (AML), associated with a high relapse rate and short disease-free survival. The oncogenic kinase Pim-1 is upregulated downstream of FLT3-ITD and contributes to its proliferative and anti-apoptotic effects. We recently showed that Pim kinase inhibition sensitizes AML cells with FLT3-ITD to apoptosis induction by topoisomerase 2 (TOP-2) inhibitors by increasing DNA double-strand breaks (DSBs) and oxidative stress. Here, we studied whether altered DSB repair activity contributes to the increase in DNA damage. Methods: Ba/F3 cells expressing FLT3-ITD (Ba/F3-ITD) or wild-type FLT3 (Ba/F3-WT) were studied. The pan-Pim kinase inhibitor AZD1208 was provided by AstraZeneca. TOP-2 inhibitors included daunorubicin (DNR), mitoxantrone (MXR) and etoposide (VP-16). Nuclear expression of repair proteins was measured by immunoblotting. Functional changes in DSB repair activities were measured in cell lines with stable chromosomal integration of the green fluorescent protein (GFP)-based DSB repair reporters DR-GFP, EJ5-GFP and EJ2-GFP, measuring homologous recombination (HR), classical non-homologous end-joining (C-NHEJ) and alternative (Alt-) NHEJ, respectively. Results: Nuclear expression of the HR component Rad51 decreased progressively (to 40%) in Ba/F3-ITD cells after 12 hours of co-treatment with AZD1208 and DNR, compared to DNR alone. Progressive decrease (to 60%) in nuclear expression of the Alt-NHEJ component DNA ligase 3 and the C-NHEJ component Ku-70 was also seen with combination treatment. Functionally, co-treatment with AZD1208 and DNR led to a 50% decrease in Alt-NHEJ repair activity, compared to DNR alone, but no significant change in C-NHEJ or HR repair activity. Ba/F3-WT cells did not show a significant change in Alt-NHEJ, HR or C-NHEJ activity with combination treatment. Decreased Alt-NHEJ activity was also seen in Ba/F3-ITD, but not Ba/F3-WT, cells co-treated with AZD1208 and MXR or VP-16. Conclusions: While nuclear expression of multiple DNA DSB repair proteins decreased, only Alt-NHEJ repair activity decreased in FLT3-ITD cells co-treated with Pim kinase and TOP-2 inhibitors. Alt-NHEJ, a highly error-prone DNA DSB repair pathway, is upregulated in cells with FLT3-ITD and contributes to genomic instability in these cells. Decreasing Alt-NHEJ repair activity in cells treated with TOP-2 inhibitors has the potential to decrease the genomic instability that may contribute to disease progression in AML patients with FLT3-ITD. Citation Format: Kshama A. Doshi, Pratik K. Nagaria, Adriana E. Tron, Feyruz V. Rassool, Maria R. Baer. Concurrent treatment with Pim kinase inhibitor decreases alternative non-homologous end-joining repair of DNA damage induced by topoisomerase 2 inhibitors in cells with FLT3-ITD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4145. doi:10.1158/1538-7445.AM2017-4145

Cockayne syndrome group B protein regulates DNA double-strand break repair and checkpoint activation.

Mutations of CSB account for the majority of Cockayne syndrome (CS), a devastating hereditary disorder characterized by physical impairment, neurological degeneration and segmental premature aging. Here we report the generation of a human CSB-knockout cell line. We find that CSB facilitates HR and represses NHEJ. Loss of CSB or a CS-associated CSB mutation abrogating its ATPase activity impairs the recruitment of BRCA1, RPA and Rad51 proteins to damaged chromatin but promotes the formation of 53BP1-Rif1 damage foci in S and G2 cells. Depletion of 53BP1 rescues the formation of BRCA1 damage foci in CSB-knockout cells. In addition, knockout of CSB impairs the ATM- and Chk2-mediated DNA damage responses, promoting a premature entry into mitosis. Furthermore, we show that CSB accumulates at sites of DNA double-strand breaks (DSBs) in a transcription-dependent manner. The kinetics of DSB-induced chromatin association of CSB is distinct from that of its UV-induced chromatin association. These results reveal novel, important functions of CSB in regulating the DNA DSB repair pathway choice as well as G2/M checkpoint activation.

Cooperation of Blm and Mus81 in development, fertility, genomic integrity and cancer suppression.

BLM is a DNA helicase important for the restart of stalled replication forks and for homologous recombination (HR) repair. Mutations of BLM lead to Bloom Syndrome, a rare autosomal recessive disorder characterized by elevated levels of sister chromatid exchanges (SCEs), dwarfism, immunodeficiency, infertility and increased cancer predisposition. BLM physically interacts with MUS81, an endonuclease involved in the restart of stalled replication forks and HR repair. Herein we report that loss of Mus81 in Blm hypomorph mutant mice leads to infertility, and growth and developmental defects that are not observed in single mutants. Double mutant cells and mice were hypersensitive to Mitomycin C and γ-irradiation (IR) compared with controls and their repair of DNA double-strand breaks (DSBs) mediated by HR pathway was significantly defective, whereas their non-homologous-end-joining repair was elevated compared with controls. We also demonstrate the importance of the loss of the nuclease activity of Mus81 in the defects observed in Mus81(-/-) and double mutant cells. Exacerbated IR-induced chromosomal aberration was observed in double mutant mice and despite their reduced SCE levels, these mutants showed increased tumorigenesis risks. Our data highlight the importance of Mus81 and Blm in DNA DSB repair pathways, fertility, development and cancer.

DNA DSB repair pathway choice: an orchestrated handover mechanism

DNA double strand breaks (DSBs) are potential lethal lesions but can also lead to chromosome rearrangements, a step promoting carcinogenesis. DNA non-homologous end-joining (NHEJ) is the major DSB rejoining process and occurs in all cell cycle stages. Homologous recombination (HR) can additionally function to repair irradiation-induced two-ended DSBs in G2 phase. In mammalian cells, HR predominantly uses a sister chromatid as a template for DSB repair; thus HR functions only in late S/G2 phase. Here, we review current insight into the interplay between HR and NHEJ in G2 phase. We argue that NHEJ represents the first choice pathway, repairing approximately 80% of X-ray-induced DSBs with rapid kinetics. However, a subset of DSBs undergoes end resection and repair by HR. 53BP1 restricts resection, thereby promoting NHEJ. During the switch from NHEJ to HR, 53BP1 is repositioned to the periphery of enlarged irradiation-induced foci (IRIF) via a BRCA1-dependent process. K63-linked ubiquitin chains, which also form at IRIF, are also repositioned as well as receptor-associated protein 80 (RAP80), a ubiquitin binding protein. RAP80 repositioning requires POH1, a proteasome component. Thus, the interfacing barriers to HR, 53BP1 and RAP80 are relieved by POH1 and BRCA1, respectively. Removal of RAP80 from the IRIF core is required for loss of the ubiquitin chains and 53BP1, and for efficient replication protein A foci formation. We propose that NHEJ is used preferentially to HR because it is a compact process that does not necessitate extensive chromatin changes in the DSB vicinity.

Repair of radiation damage of U2OS osteosarcoma cells is related to DNA-dependent protein kinase catalytic subunit (DNA-PKcs) activity

The present study was to investigate the effects of DNA-PKcs deficiencies on radiation sensitivity of human osteosarcoma U2OS cells to γ-ray and to explore the underlying molecular mechanism. In vitro, U2OS cells were transfected with different DNA-PKcs siRNAs or control siRNAs to establish stably siRNA-transfected cell lines U2OS-Si and U2OS-Sc, respectively. Cell viability and apoptosis after irradiation were analyzed using cell counting kit (CCK-8) and flow cytometric assay, respectively. Expressions of apoptosis-related and oxidative stress-responded proteins were assessed using Western blot. The tumorigenesis activity was examined in nude mice xenograft osteosarcoma mode. Results showed that DNA-PKcs siRNA significantly could inhibit U2OS viability and cell proliferation after exposure to irradiation. Compared with the U2OS and U2OS-Sc cells, the U2OS-Si cells induced higher apoptosis rate and loss of mitochondrial membrane potentials, accompanying with more reactive oxygen species (ROS) and malondialdehyde (MDA) production, increased DNA double-strand breaks (DSBs) induced by irradiation. Protein levels of the anti-apoptotic Bcl-2 were downregulated most obviously in U2OS-Si cells after irradiation, while pro-apoptotic factor Bax and caspase-3 upregulated. Moreover, the antioxidants protein expression levels of Nuclear factor-erythroid 2-related factor 2 (Nrf2) and its target heme oxygenase-1 (HO-1) were also significantly reduced in parallel to DNA-PKcs inhibition in U2OS-Si cells. In nude mice xenograft model, DNA-PKcs siRNA remarkably inhibited tumor growth and dissemination. In conclusion, DNA-PKcs siRNA might have a potential for osteosarcoma treatment by sensitizing osteosarcoma cells to γ-ray through modulation on oxidative stress-mediated DNA DSBs repair and mitochondrial pathway apoptosis.

Benzo[a]pyrene increases DNA double strand break repair in vitro and in vivo: A possible mechanism for benzo[a]pyrene-induced toxicity

Benzo[a]pyrene (BaP) is a polycyclic aromatic hydrocarbon and carcinogen that is released into the environment through natural and anthropogenic sources. BaP toxicity is dependent on its metabolism by cytochrome P450s to the reactive metabolite benzo[a]pyrene diol epoxide (BPDE), which is strongly associated with increased mutation frequency. BaP can also be metabolized to benzo[a]pyrene quinones that can undergo redox cycling and induce oxidative stress. The purpose of this study was to examine if BaP exposure induces DNA double strand breaks (DSBs) and subsequently activate DNA DSB repair pathways in the CHO 3–6 cell line and pKZ1 mouse model. In vitro assessment of homologous recombination (HR) showed significantly increased HR frequency following exposure to 10μM of BaP. In vivo evaluations of BaP-induced DNA DSB repair demonstrated positive staining for intrachromosomal recombination events, which are associated with non-homologous end joining (NHEJ), in the lung and thymus of exposed animals that were statistically significant in the thymus when quantified by Western blotting. Gene expression analyses from mouse tissues showed significantly decreased expression of ATM and Xrcc6 in BaP-treated liver and lung. In addition, BaP exposure significantly reduced the expression of Xrcc5, p53, and DNA-PKcs in lung. Taken together, our results demonstrate that BaP increases DNA DSB repair in vitro and in vivo, and induces expression changes in DNA repair pathway genes. As repair of DNA DSBs is not error-free, aberrant DNA repair may be contributing to the mechanism of BaP-induced toxicity.

Inhibition of Ku70 acetylation by INHAT subunit SET/TAF-Iβ regulates Ku70-mediated DNA damage response.

DNA double-strand breaks (DSBs) can cause either cell death or genomic instability. The Ku heterodimer Ku70/80 is required for the NHEJ (non-homologous end-joining) DNA DSB repair pathway. The INHAT (inhibitor of histone acetyltransferases) complex subunit, SET/TAF-Iβ, can inhibit p300- and PCAF-mediated acetylation of both histone and p53, thereby repressing general transcription and that of p53 target genes. Here, we show that SET/TAF-Iβ interacts with Ku70/80, and that this interaction inhibits CBP- and PCAF-mediated Ku70 acetylation in an INHAT domain-dependent manner. Notably, DNA damage by UV disrupted the interaction between SET/TAF-Iβ and Ku70. Furthermore, we demonstrate that overexpressed SET/TAF-Iβ inhibits recruitment of Ku70/80 to DNA damage sites. We propose that dysregulation of SET/TAF-Iβ expression prevents repair of damaged DNA and also contributes to cellular proliferation. All together, our findings indicate that SET/TAF-Iβ interacts with Ku70/80 in the nucleus and inhibits Ku70 acetylation. Upon DNA damage, SET/TAF-Iβ dissociates from the Ku complex and releases Ku70/Ku80, which are then recruited to DNA DSB sites via the NHEJ DNA repair pathway.

Role Of Sirtuin-6 In Maintenance Of Genomic Instability In Multiple Myeloma Cells

BackgroundDeregulation of the DNA damage response (DDR) signaling machinery underlies genomic instability, leading to cancer development and clonal evolution. Multiple Myeloma (MM) remains an incurable disease characterized by a highly unstable genome, with aneuploidy observed in nearly all patients. The mechanism causing this karyotypic instability is largely unknown, but recent observations have correlated these abnormalities with dysfunctional DDR machinery. Mammalian NAD+-dependent deacetylase sirtuin-6 (SIRT6) is emerging as new protein involved in multiple pathways, including maintenance of genome integrity. MethodsA panel of 18 MM cell lines, both sensitive and resistant to conventional and novel anti-MM therapies, was used in this study. Blood and BM samples from healthy volunteers and MM patients were obtained after informed consent and mononuclear cells (MNCs) separated by Ficoll-Paque density sedimentation. Patient MM cells were isolated from BM MNCs by CD138-positive selection. Lentiviral delivery was used for expression and knock-down of SIRT6 in MM cell lines. The biologic impact of SIRT6 phenotype was evaluated using cell growth, viability and apoptosis assays. DNA Double-Strand Breaks (DSB) repair occurring via homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways was assessed using a transient direct repeat (DR)-GFP/I-SceI system. ResultsA comparative gene expression analysis of 414 newly-diagnosed uniformly-treated MM patients showed high levels of SIRT6 mRNA in MM patients versus MGUS or normal donors; moreover, in active MM elevated SIRT6 expression correlated with adverse clinical outcome. Due to its prognostic significance, we further evaluated its role in MM biology. We found higher SIRT6 nuclear expression in MM cell lines and primary cells compared to PBMCs from healthy donors. Targeting SIRT6 by specific shRNA increased MM cell survival by reducing DNA repair efficiency (HR and NHEJ). Whole genome profiling of three different SIRT6 knockout (Sirt6-/-) MM cell lines identified a restricted effect of SIRT6 silencing on transcription of DNA damage genes, which also represented the most down-regulated genes. Consistent with these data, GSEA algorithm revealed that gene set regulating DNA repair were prominently enriched in SIRT6 depleted cells (p<0.0001 and FDR=0.003), confirming the role of SIRT6 in this pathway. We next examined the therapeutic relevance of SIRT6 inhibition in MM by evaluating the effect of SIRT6 depletion on cytotoxicity induced by genotoxic agents. SIRT6 shRNA impaired DNA DSB repair pathways triggered by DNA damaging agents, thereby enhancing overall anti-MM activity of these agents. Finally, in concert with our in vitro data, studies using our human MM xenograft model confirmed that SIRT6 depletion enhanced anti-MM activity of DNA-damaging agents. ConclusionCollectively, our data provide basis for targeting SIRT6 as a novel therapeutic strategy in combination with genotoxic agents to enhance cytotoxicity and improve patient outcome in MM. Disclosures:Tai:Onyx: Consultancy. Hideshima:Acetylon Pharmaceuticals: Consultancy. Chauhan:Vivolux: Consultancy. Anderson:celgene: Consultancy; onyx: Consultancy; gilead: Consultancy; sanofi aventis: Consultancy; oncopep: Equity Ownership; acetylon: Equity Ownership.

Misrepair of DNA double-strand breaks after exposure to heavy-ion beams causes a peak in the LET–RBE relationship with respect to cell killing in DT40 cells

To determine the radiobiological mechanisms underlying relative biological effectiveness (RBE) and the repair efficiencies of DNA double-strand breaks (DSBs) as a function of linear energy transfer (LET), we exposed cells of the chicken B-lymphocyte cell line DT40 and its DSB repair pathway-deficient derivatives to heavy-ion beams produced at the Heavy-Ion Medical Accelerator in Chiba (HIMAC) at the National Institute of Radiological Sciences (NIRS), Chiba, Japan. The relationship between LET and cell lethality was investigated in the DNA DSB repair gene knockouts Ku70−/−, Rad54−/−, and Ku70−/−Rad54−/−, and in the wild-type cells. We found that cell-cycle stage and activity of the DNA DSB repair pathways influence LET-mediated biological effects. An expected LET–RBE relationship was observed in the cells capable of DNA repair, but no peak was found in the RBE with respect to cell survival in the Ku70−/−Rad54−/− cells or in Ku70−/− cells in the G1 and early S cell-cycle phases (when no sister chromatids were present and homologous recombination could not occur). These findings suggest that the peak in RBE is caused by deficient repair of the DNA DSBs.

Abstract 1583: Proteasome inhibition as a strategy for non-small cell lung carcinoma via inhibition of DNA double strand break repair.

Abstract Background: Each year, ∼60,000 US patients are diagnosed with locally advanced non-small cell lung carcinoma (NSCLC). Despite optimal radiation therapy (RT), chemotherapy +/- surgery, over 30% of patients fails locoregionally. The addition of concurrent chemotherapy to RT adds only ∼5% absolute survival benefit. Novel radiosensitizers may improve the therapeutic index. To identify the best potential targets, we performed whole genome RNAi screens that identified several proteasome subunits among top genes whose knockdown increased NSCLC cytotoxicity. Materials and Methods: Cytotoxicity was assessed by luminescent cell viability and clonogenic assays. Homologous recombination (HR) and non-homologous end-joining (NHEJ) were assessed using NSCLC cell lines transduced with reporter constructs that express GFP upon repair of I-SceI-induced DNA double strand breaks (DSBs). DNA damage-induced focus formation was assessed by immunofluorescence, scoring % of cells showing ≥5 foci. In vivo radiosensitization by proteasome gene knockdown was assessed using NCr nude mice injected with 1x106 NCI-H460 cells stably transfected with inducible PSMA1 shRNA. Once tumors reached ≥3 mm, knockdown was induced with doxycycline, and then one week later, RT to a dose of 20 Gy in 5 fractions was initiated. Results: Radiation and proteasome inhibition showed synergistic cytotoxicity. Irradiation of A549 cells with 1 Gy x 3 decreased clonogenic survival by 58% compared to control, while ionizing radiation (IR) plus 10 nM bortezomib decreased survival by 74% compared to bortezomib alone. Similar results were seen in NCI-H460. Proteasome inhibition via bortezomib or PSMA1 siRNA knockdown resulted in 80-90% decreased HR and NHEJ. Additionally, bortezomib or PSMA1 shRNA knockdown resulted in ≥50% decreases in BRCA1, FANCD2 or RAD51 IR-induced focus formation. Treatment of NCI-H460 xenografts with RT in the setting of PSMA1 knockdown showed marked improvements in survival; at 100 days post treatment initiation, only 20% of RT-only treated mice and 30% of doxycycline-treated mice (for PSMA1 shRNA knockdown in tumors) survived, compared to 100% following dual treatment (n = 10 per arm). There was a statistically significant difference in survival between mice with tumors treated with RT alone vs. RT + PSMA1 knockdown, with median survivals of 43 days vs. not reached, P = .0003 by the log-rank test. Conclusions: Proteasome inhibition has emerged as a promising target in NSCLC radiosensitization with evidence indicating the mechanism is through inhibition of DNA DSB repair pathways HR and NHEJ. Citation Format: Kyle R. Cron, Kaya Zhu, Deepa Kushwaha, Grace Hsieh, Dmitry Merzon, Jack Monahan, Clark C. Chen, Alan D'Andrea, David Kozono. Proteasome inhibition as a strategy for non-small cell lung carcinoma via inhibition of DNA double strand break repair. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1583. doi:10.1158/1538-7445.AM2013-1583

PARP activation regulates the RNA-binding protein NONO in the DNA damage response to DNA double-strand breaks

After the generation of DNA double-strand breaks (DSBs), poly(ADP-ribose) polymerase-1 (PARP-1) is one of the first proteins to be recruited and activated through its binding to the free DNA ends. Upon activation, PARP-1 uses NAD+ to generate large amounts of poly(ADP-ribose) (PAR), which facilitates the recruitment of DNA repair factors. Here, we identify the RNA-binding protein NONO, a partner protein of SFPQ, as a novel PAR-binding protein. The protein motif being primarily responsible for PAR-binding is the RNA recognition motif 1 (RRM1), which is also crucial for RNA-binding, highlighting a competition between RNA and PAR as they share the same binding site. Strikingly, the in vivo recruitment of NONO to DNA damage sites completely depends on PAR, generated by activated PARP-1. Furthermore, we show that upon PAR-dependent recruitment, NONO stimulates nonhomologous end joining (NHEJ) and represses homologous recombination (HR) in vivo. Our results therefore place NONO after PARP activation in the context of DNA DSB repair pathway decision. Understanding the mechanism of action of proteins that act in the same pathway as PARP-1 is crucial to shed more light onto the effect of interference on PAR-mediated pathways with PARP inhibitors, which have already reached phase III clinical trials but are until date poorly understood.